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import os
from io import StringIO
import ase.io as aio
from ase.io.gromacs import read_gromacs, write_gromacs
def test_gromacs_1():
standard_gromacs = '''MD of 2 waters, t= 0.0
6
1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
1WATER HW2 2 0.190 1.661 1.747 0.8085 0.3191 -0.7791
1WATER HW3 3 0.177 1.568 1.613 -0.9045 -2.6469 1.3180
2WATER OW1 4 1.275 0.053 0.622 0.2519 0.3140 -0.1734
2WATER HW2 5 1.337 0.002 0.680 -1.0641 -1.1349 0.0257
2WATER HW3 6 1.326 0.120 0.568 1.9427 -0.8216 -0.0244
1.82060 1.82060 1.82060
'''
# read x from StringIO
gromacs_file = StringIO(standard_gromacs)
x = read_gromacs(gromacs_file)
# write x to StringIO
out_stringio = StringIO()
write_gromacs(out_stringio, x)
out_stringio.seek(0)
# verify
output = out_stringio.read()
ase_output = '\n'.join(output.split('\n')[1:-2])
standard_output = '\n'.join(standard_gromacs.split('\n')[1:-2])
# import pdb; pdb.set_trace()
assert (ase_output == standard_output
), 'ASE gromacs output differs from standard output'
def test_gromacs_2(tmp_path: str):
water_str = """water
3
1SOL OW000 1 0.000 0.000 0.000
1SOL HW001 2 0.000 0.100 0.000
1SOL HW002 3 0.088 -0.036 0.000
1.00000 1.00000 1.00000\n"""
gro_file = os.path.join(tmp_path, "water.gro")
with open(gro_file, "w") as f:
f.write(water_str)
ase_atoms = read_gromacs(gro_file)
assert str(ase_atoms.symbols) != "W3"
byte_atoms = read_gromacs(gro_file)
assert str(byte_atoms.symbols) == "OH2"
dump_gro_file = os.path.join(tmp_path, "dump_water.gro")
aio.write(dump_gro_file, byte_atoms)
reload_atoms = read_gromacs(dump_gro_file)
for atom_a, atom_b in zip(byte_atoms, reload_atoms):
assert atom_a.symbol == atom_b.symbol
assert all(atom_a.position == atom_b.position)
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